Specify 7.1 Major Update–WorkBench for the Web

Specify 7.1 Release Notes

Specify 7.1 is a significant update to the Specify web platform for collection curation and data management–it implements the Specify WorkBench. Like the WorkBench in Specify 6, this Specify 7 version enables batch data entry for Collection Object and other types of data records, but within a web browser. With a web version of the WorkBench, batch data entry and editing can be done from any networked computer with a web browser, and without the need to install additional software.

Specify 7.1 is available from the Specify 7 GitHub open source repository (https://github.com/specify/specify7). Hosted Specify Cloud institutions have been upgraded to the new release.

The Specify WorkBench module is commonly used for production-level digitization of specimen information. The batch data processing format enables project managers to stage and inspect incoming specimen records before they are uploaded to the Specify repository.
Like the rest of Specify 7, the new WorkBench module operates entirely inside of a web browser window. It creates data sets which can be edited, validated and saved before uploading into a Specify database on a local or remote cloud server. The Specify 7.1 WorkBench is integrated with a new web version of Specify’s schema mapper tool to enable custom mapping of import file data columns to Specify’s database schema. Its data mapping capability is the same as in Specify 6; it enables WorkBench DataSet templates to be defined which contain only the data fields required for import into a Specify collection database. The Specify 7.1 web WorkBench also imports and exports data in CSV format files. Importing external files is useful for moving information from Excel spreadsheets into Specify through the WorkBench.

Specify 6 (thick client) and 7 (web) are open source and available at no cost. For additional information, see the Specify Project Web Site (http://www.specifysoftware.org). U.S. biological research collections are eligible for technical support and related legacy data conversion and software customization services.

Specify 7 WorkBench (WB)—Capabilities and Web Usage

Like the WorkBench in Specify 6, the Specify 7 WB enables batch data entry for Collection Object and other types of database records, but within a web browser. The Specify WorkBench module is commonly used for production-level digitization of specimen information. The batch data processing format enables project managers to stage and inspect incoming specimen records before they are uploaded to the Specify repository.

The Specify 7 WB supports: imports of external data files (CSV format), new DataSet (and Data Mapping) creation, DataSet editing, record validation, and exporting DataSets to external CSV format files.

In Specify 7, newly entered or edited WorkBench DataSet data are not saved until the “Save” button located above the WB is pushed.

When using Specify 7, closing a WB browser window, stopping the web browser application, or powering down the computer will lose changes (edits/additions) to a DataSet since the last Save.

While editing a WorkBench dataset clicking on the web browser BACK button or Left Arrow will close the window and the Specify DataSet without saving. Any changes made to the DataSet since the last WorkBench “Save” will be lost.

Save often when editing a single WorkBench DataSet for an extended period.

A WorkBench DataSet should not be edited in more than one browser window at the same time, otherwise data will be lost. If users makes changes to the same WorkBench DataSet open in two or more browser windows, only the last WorkBench Dataset saved will be recorded.

For example,

  • If edits are made to records 1, 2, 3 in a DataSet, in web browser tab #1, and
  • Additions (or edits) are made to records 4, 5, 6 in open browser tab #2 , then
  • Two different versions of the DataSet will exist—multiple browser copies of the same DataSet are not synchronized. Copies of the same DataSet in different browser tabbed windows are independent of one another.
  • If the DataSet in tab #2 is saved, contents of the DataSet in tab #1 are not affected.
  • If the DataSet in tab #1 is then saved, changes made to the DataSet (previously saved) from browser tab #2 are permanently overwritten and lost.

Remember, when two or more copies of the same WorkBench DataSet are open, the last copy saved is the only version with saved changes–edits and additions in other previously saved DataSet copies are lost.

We strongly recommend not opening the same WorkBench DataSet in more than one browser window.

Differences between the Specify 6 and 7 WorkBench modules

  1. WorkBench data mapping templates can be created in Specify 7, but cannot be changed in 7, once saved. Specify 7 data mapping templates can be modified in Specify 6. Mappings created and edited in 6 can be used in 7.
  2. The Specify 7 WorkBench currently does not have the capability found in Specify 6 to attach external files (e.g. images) to WorkBench Collection Object records to then be uploaded. But like 6, Specify 7 allows files including images to be attached to records once they are created in the database through the Specify 7 (web) form interface.
  3. In the Specify 7 WorkBench records can be exported to CSV format files for external use or for sending to other Specify users as files. CSV file transfers do not include schema mappings, unlike Excel format file exports from the Specify 6 WorkBench. If you plan to move Specify 7 WorkBench DataSet CSV export files to another user, the recipient must remap the data set using the same schema mapping used to create the DataSet then import it.
  4. Specify 7 WB does not currently support the carry-forward function for creating new records.
  5. Specify 7 WB does include the fill-down capability found in Specify 6 and Excel (i.e. one can select a cell and then ‘pull down’ to fill cells with the same value in subsequent records).
  6. Specify 7 WB can fill multiple columns at the same time by highlighting cells in two or more adjacent columns and then by ‘pulling down’.
  7. The Specify 7 WorkBench, unlike Specify 6 does not auto-increment Catalog Numbers when selecting and ‘pulling down’ a highlighted Catalog Number cell. If Specify is configured to require sequential catalog number values to be entered for importing records, they will need to be keystroked into the Specify 7 WB for each record.
  8. The Autofill capability available in Specify 6 is not yet available in the Specify 7 WorkBench. Autofill allows Catalog Number fields to be left blank in DataSets and upon upload Specify determines the next available Catalog Numbers from the database.
  9. GeoLocate and Google Earth are not yet integrated into the Specify 7 WorkBench.
  10. The Coordinate Convertor function with Latitude and Longitude data fields is not available in Specify 7.
  11. The Specify 7 WorkBench has no form view option, unlike Specify 6.
  12. Specify 7 does not allow viewing of WorkBench data in Specify data forms before committing, unlike Specify 6.
  13. Data validation checking in Specify 7 is handled differently from the way it operates in Specify 6 WorkBench uploads. In 7, data values are not checked immediately upon keystroke entry into a WorkBench cell, but record contents for the entire WorkBench are validated in batch mode, which can be done at any time by using the “Validate” button.
  14. Several WorkBench-to-Specify upload preferences are not supported currently in Specify 7. In Specify 6, the upload function can be set to respond to situations where parts or components of a new WB Collection Object record match two or more existing records in the database. During uploads from the WorkBench to the Specify database, Specify attempts to match existing data field values to those values being imported. For example if a Taxon record already exists for the genus and species being uploaded, Specify will simply link that new Collection Object record to the existing Taxon. Similar attempts are made for data in Geography, Locality and Agent data fields. Occasionally the contents of a data field being uploaded will match more than one existing record. During the upload process if Specify 6 encounters a match with two or more existing records in those tables, it provides the user with several options to resolve the situation:
    • Skip — Ignore the Collection Object record completely, do not upload, and leave in WB.
    • Add – Create a new record in the Specify table with two or more matching records
    • Choose First — Match the first record in whichever table contains duplicate matches
    • Choose Match – Display a choice of records to match on the screen for the user to pick
    • Match Empty Cells — Require empty cells in WB to only match empty fields in Specify

    These upload matching preferences are not yet available in the Specify 7. We will continue to develop and enhance Specify 7 WorkBench capabilities for future releases.